problems with stitching images

[Trowbridge <Trowbridge@xxxxxxxxx>]

Can anyone help with a problem I am having when stitching images? I scan my
35mm Widelux transparencies as left and right hand pieces using the cut film
holder on a Nikon Coolscan II.  Then I crop to a convenient point and
stitch.  I've just started to use color negative film, and the scanner is
giving a color imbalance between the two scans.  I've put an example on my
web page: http://homepages.tesco.net/~trowbridge/stitch.htm
I presume the scanner software is inverting the image and removing the
orange mask. But why the inconsistency?
Any observations would be gratefully received.
Regards
IanT